There is a need to automate capillary LC/MS systems for use in applications which require pre-concentration. Prior automated μLC/MS/MS systems employ trapping/pre-concentration columns integrated with the separation column through transfer lines. However, the integration of the trap with an analysis column which operates at very low flow rates (200 nanoliters per minute and less) presents special challenges.
Capillary LC-MS/MS systems operating at very low flow rates can be automated by using an autosampler to load a peptide trap at higher flow rates in the range from 0.5 to 500 microliters per minute, and preferably in the range from 5- to 50 microliters per minute. After washing, a valve connects the trap on-line with the LC column at a slower rate from 10 to 1,000 nanoliters per minute, and preferably at about 200 nanoliters per minute. An on-line mass spectrometer is used to detect the chromatography eluent from the analysis column. While this technique has been automated, the resulting systems have been characterized by large extra-column volumes and other problems.